[BioC] makeTranscriptDbFromBiomart error

Stefanie stefanie.tauber at univie.ac.at
Wed Jun 6 16:03:24 CEST 2012


Hi,

here is my code:
library(GenomicFeatures)
humanDB = makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"hsapiens_gene_ensembl")

This is the error I get thrown:
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... Fehler in
.extractCdsRangesFromBiomartTable(bm_table) : 
  BioMart data anomaly: some 5' UTR have a start > end

Seems to be a problem of biomart not of R?
Anybody any idea?

Best,
Stefanie

sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.6.5 AnnotationDbi_1.16.10 Biobase_2.14.0       
GenomicRanges_1.6.4   IRanges_1.12.5        biomaRt_2.10.0       

loaded via a namespace (and not attached):
[1] Biostrings_2.22.0  BSgenome_1.22.0    DBI_0.2-5          RCurl_1.8-0       
RSQLite_0.11.1     rtracklayer_1.14.4 tools_2.14.1       XML_3.6-2         
[9] zlibbioc_1.0.0



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